What looks like a redundant prosecution is in fact something worse. It is an unconstitutional attempt to federalize a crime that South Carolina's courts are perfectly capable of handling on their own, for the sake of sending a message that the criminal law should not be used to send.
The New York Times reports that "Justice Department and FBI officials have said the Charleston shooting was so horrific and racially motivated that the federal government must address it." The Times notes that "South Carolina does not have a hate crime law," adding that "federal officials have said they believe that a murder case alone would leave the racial component of the crime unaddressed."
In other words, by charging Roof with murdering people "because of their actual and perceived race and color," the Justice Department condemns his benighted beliefs, as well as his appalling actions. The Times notes that the evidence against Roof includes his "racist Internet manifesto," as well as his anti-black comments as he shot the parishioners at the church.
Because Roof already faces the maximum penalty under state law, he can hardly receive extra punishment for his bigotry. But defendants in less serious cases can and do: An assault that might be punished by a year or two in prison under state law can trigger a sentence up to 10 years under the federal hate crime statute if the defendant has a history of writing or saying racist stuff.
In fact, the offender in such a case can be punished twice for the same crime, once under state law and again under federal law. And if he happens to be acquitted in state court, he can be tried again in federal court.
This sort of serial prosecution looks an awful lot like double jeopardy, which is prohibited by the Fifth Amendment. But according to the Supreme Court, it is merely "dual sovereignty": The same action is two crimes, one for each government that has jurisdiction.
You may wonder where Congress got the authority to federalize a crime based on the nasty opinions expressed by the person who committed it. The provision under which Roof was charged, which applies to cases where the victim was chosen because of his "actual or perceived race, color, religion or national origin," is supposedly authorized by the 13th Amendment.
If you do not understand how the constitutional ban on slavery applies to someone who punches an African-American or a Latino while shouting a racial epithet, or to someone who specializes in mugging Jews because he figures they have a lot of money, you are not alone. As the Cato Institute and the Reason Foundation (my employer) noted in a 2013 Supreme Court brief, the provision cited in Roof's federal indictment "does not prohibit slavery or involuntary servitude"; "nor is it a prophylactic measure intended to assist in preventing the return of slavery or involuntary servitude."
The constitutional rationale for another provision of the federal hate crime law, covering crimes in which the victims were selected because of their "gender, sexual orientation, gender identity or disability," is even less plausible. All it takes to make a federal case out of such crimes is a weapon "that has traveled in interstate or foreign commerce."
The farcical justifications for the federal hate crime statute are especially troubling because there is no reason to think the offenders it covers would otherwise go unpunished. If the Charleston massacre is exactly the sort of crime the law was meant to address, that just shows how gratuitous the law is.